Multiple sequence alignment - TraesCS5D01G540100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G540100 chr5D 100.000 3241 0 0 1 3241 551446885 551450125 0.000000e+00 5986.0
1 TraesCS5D01G540100 chr5D 94.290 2154 95 7 814 2961 552042541 552040410 0.000000e+00 3271.0
2 TraesCS5D01G540100 chr5D 85.175 1113 132 20 825 1930 552422786 552421700 0.000000e+00 1110.0
3 TraesCS5D01G540100 chr5D 82.935 1213 148 27 788 1984 552458418 552457249 0.000000e+00 1038.0
4 TraesCS5D01G540100 chr5D 86.697 669 68 10 1963 2631 552456809 552456162 0.000000e+00 723.0
5 TraesCS5D01G540100 chr5D 74.330 1305 237 66 827 2076 551057626 551058887 6.330000e-127 464.0
6 TraesCS5D01G540100 chr5D 73.080 1393 276 71 798 2147 543465668 543464332 1.400000e-108 403.0
7 TraesCS5D01G540100 chr5D 78.856 577 109 11 842 1411 551611496 551612066 8.490000e-101 377.0
8 TraesCS5D01G540100 chr5D 83.120 391 39 11 226 590 552043043 552042654 6.700000e-87 331.0
9 TraesCS5D01G540100 chr5D 81.818 220 40 0 1191 1410 551081983 551082202 5.520000e-43 185.0
10 TraesCS5D01G540100 chr5B 93.722 2198 99 14 460 2631 700237956 700235772 0.000000e+00 3258.0
11 TraesCS5D01G540100 chr5B 84.517 1253 152 25 753 1984 698256481 698257712 0.000000e+00 1201.0
12 TraesCS5D01G540100 chr5B 95.447 637 25 3 1928 2562 699945407 699946041 0.000000e+00 1013.0
13 TraesCS5D01G540100 chr5B 77.562 1542 285 43 760 2273 685499422 685500930 0.000000e+00 874.0
14 TraesCS5D01G540100 chr5B 86.677 668 61 11 1963 2622 698258136 698258783 0.000000e+00 715.0
15 TraesCS5D01G540100 chr5B 74.672 533 106 17 1513 2030 703540144 703540662 3.280000e-50 209.0
16 TraesCS5D01G540100 chr5B 74.453 548 96 30 798 1337 699435526 699436037 2.550000e-46 196.0
17 TraesCS5D01G540100 chr5B 98.958 96 1 0 1 96 700238100 700238005 4.300000e-39 172.0
18 TraesCS5D01G540100 chr5B 98.958 96 1 0 1 96 700242364 700242269 4.300000e-39 172.0
19 TraesCS5D01G540100 chr5B 98.551 69 1 0 2863 2931 700235461 700235393 4.390000e-24 122.0
20 TraesCS5D01G540100 chr5B 94.118 51 3 0 226 276 699945287 699945337 9.640000e-11 78.7
21 TraesCS5D01G540100 chr5B 87.931 58 3 3 14 71 699945232 699945285 7.510000e-07 65.8
22 TraesCS5D01G540100 chr4A 95.629 1853 57 7 1080 2925 616674841 616673006 0.000000e+00 2952.0
23 TraesCS5D01G540100 chr4A 73.985 1626 318 68 825 2390 616618700 616617120 2.180000e-156 562.0
24 TraesCS5D01G540100 chr4A 77.453 581 98 22 831 1404 616897507 616896953 1.880000e-82 316.0
25 TraesCS5D01G540100 chr4A 85.664 286 17 3 156 441 616675233 616674972 2.460000e-71 279.0
26 TraesCS5D01G540100 chr4A 84.722 144 20 1 2727 2868 616869072 616868929 3.370000e-30 143.0
27 TraesCS5D01G540100 chr4A 86.420 81 9 2 2528 2608 616869321 616869243 1.600000e-13 87.9
28 TraesCS5D01G540100 chr2B 81.556 450 74 6 1483 1927 798913616 798913171 2.380000e-96 363.0
29 TraesCS5D01G540100 chr4B 97.143 35 1 0 1401 1435 663402740 663402706 3.490000e-05 60.2
30 TraesCS5D01G540100 chr4B 97.143 35 1 0 1401 1435 663403663 663403697 3.490000e-05 60.2
31 TraesCS5D01G540100 chr4B 97.143 35 1 0 1401 1435 663406761 663406727 3.490000e-05 60.2
32 TraesCS5D01G540100 chr4B 91.304 46 1 3 1401 1446 663407682 663407724 3.490000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G540100 chr5D 551446885 551450125 3240 False 5986.000000 5986 100.000000 1 3241 1 chr5D.!!$F3 3240
1 TraesCS5D01G540100 chr5D 552040410 552043043 2633 True 1801.000000 3271 88.705000 226 2961 2 chr5D.!!$R3 2735
2 TraesCS5D01G540100 chr5D 552421700 552422786 1086 True 1110.000000 1110 85.175000 825 1930 1 chr5D.!!$R2 1105
3 TraesCS5D01G540100 chr5D 552456162 552458418 2256 True 880.500000 1038 84.816000 788 2631 2 chr5D.!!$R4 1843
4 TraesCS5D01G540100 chr5D 551057626 551058887 1261 False 464.000000 464 74.330000 827 2076 1 chr5D.!!$F1 1249
5 TraesCS5D01G540100 chr5D 543464332 543465668 1336 True 403.000000 403 73.080000 798 2147 1 chr5D.!!$R1 1349
6 TraesCS5D01G540100 chr5D 551611496 551612066 570 False 377.000000 377 78.856000 842 1411 1 chr5D.!!$F4 569
7 TraesCS5D01G540100 chr5B 700235393 700238100 2707 True 1184.000000 3258 97.077000 1 2931 3 chr5B.!!$R2 2930
8 TraesCS5D01G540100 chr5B 698256481 698258783 2302 False 958.000000 1201 85.597000 753 2622 2 chr5B.!!$F4 1869
9 TraesCS5D01G540100 chr5B 685499422 685500930 1508 False 874.000000 874 77.562000 760 2273 1 chr5B.!!$F1 1513
10 TraesCS5D01G540100 chr5B 699945232 699946041 809 False 385.833333 1013 92.498667 14 2562 3 chr5B.!!$F5 2548
11 TraesCS5D01G540100 chr5B 703540144 703540662 518 False 209.000000 209 74.672000 1513 2030 1 chr5B.!!$F3 517
12 TraesCS5D01G540100 chr4A 616673006 616675233 2227 True 1615.500000 2952 90.646500 156 2925 2 chr4A.!!$R3 2769
13 TraesCS5D01G540100 chr4A 616617120 616618700 1580 True 562.000000 562 73.985000 825 2390 1 chr4A.!!$R1 1565
14 TraesCS5D01G540100 chr4A 616896953 616897507 554 True 316.000000 316 77.453000 831 1404 1 chr4A.!!$R2 573

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
375 376 1.005630 GGTGCACAGAACGCTCTCT 60.006 57.895 20.43 0.0 0.00 3.10 F
1581 1715 0.726452 GCGTCGATGATCGCCTAGTC 60.726 60.000 10.45 0.0 45.54 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2730 1.156736 GAGTTGTTCCCACATCACGG 58.843 55.0 0.0 0.0 31.06 4.94 R
2984 3813 0.249238 GGTAGAGCGAGGCACATCTG 60.249 60.0 0.0 0.0 0.00 2.90 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.978978 TCCTCAGAGTTTTGGTCATCCA 59.021 45.455 0.00 0.00 42.66 3.41
97 98 3.588842 TCCTCAGAGTTTTGGTCATCCAT 59.411 43.478 0.00 0.00 43.91 3.41
98 99 3.693085 CCTCAGAGTTTTGGTCATCCATG 59.307 47.826 0.00 0.00 43.91 3.66
99 100 4.330250 CTCAGAGTTTTGGTCATCCATGT 58.670 43.478 0.00 0.00 43.91 3.21
100 101 5.491070 CTCAGAGTTTTGGTCATCCATGTA 58.509 41.667 0.00 0.00 43.91 2.29
101 102 6.065976 TCAGAGTTTTGGTCATCCATGTAT 57.934 37.500 0.00 0.00 43.91 2.29
102 103 6.484288 TCAGAGTTTTGGTCATCCATGTATT 58.516 36.000 0.00 0.00 43.91 1.89
104 105 8.274322 TCAGAGTTTTGGTCATCCATGTATTAT 58.726 33.333 0.00 0.00 43.91 1.28
105 106 8.906867 CAGAGTTTTGGTCATCCATGTATTATT 58.093 33.333 0.00 0.00 43.91 1.40
147 148 9.950496 ATTGTATTTGAAAGCTAGAGAAGAAGA 57.050 29.630 0.00 0.00 0.00 2.87
148 149 8.994429 TGTATTTGAAAGCTAGAGAAGAAGAG 57.006 34.615 0.00 0.00 0.00 2.85
149 150 8.037758 TGTATTTGAAAGCTAGAGAAGAAGAGG 58.962 37.037 0.00 0.00 0.00 3.69
150 151 6.672266 TTTGAAAGCTAGAGAAGAAGAGGA 57.328 37.500 0.00 0.00 0.00 3.71
151 152 5.652994 TGAAAGCTAGAGAAGAAGAGGAC 57.347 43.478 0.00 0.00 0.00 3.85
152 153 5.329399 TGAAAGCTAGAGAAGAAGAGGACT 58.671 41.667 0.00 0.00 0.00 3.85
153 154 5.417580 TGAAAGCTAGAGAAGAAGAGGACTC 59.582 44.000 0.00 0.00 0.00 3.36
154 155 4.584638 AGCTAGAGAAGAAGAGGACTCA 57.415 45.455 1.75 0.00 32.59 3.41
203 204 4.131088 GGCGTCGTCCTCCTCCAC 62.131 72.222 0.00 0.00 0.00 4.02
359 360 3.692406 GTGGCCTTCCTCGACGGT 61.692 66.667 3.32 0.00 0.00 4.83
367 368 1.740332 TTCCTCGACGGTGCACAGAA 61.740 55.000 24.13 8.56 0.00 3.02
375 376 1.005630 GGTGCACAGAACGCTCTCT 60.006 57.895 20.43 0.00 0.00 3.10
407 408 4.813526 CTGCTCCGTCGTCGTCCG 62.814 72.222 0.71 0.00 38.13 4.79
429 430 4.039092 ACCATCCGCAGCAGCCTT 62.039 61.111 0.00 0.00 37.52 4.35
450 451 1.151450 CCATGCCCTCCACCATACC 59.849 63.158 0.00 0.00 0.00 2.73
454 455 3.087253 CCCTCCACCATACCGCCA 61.087 66.667 0.00 0.00 0.00 5.69
455 456 2.452064 CCCTCCACCATACCGCCAT 61.452 63.158 0.00 0.00 0.00 4.40
458 459 2.028125 CTCCACCATACCGCCATCGT 62.028 60.000 0.00 0.00 0.00 3.73
463 499 1.065109 CATACCGCCATCGTCGTCA 59.935 57.895 0.00 0.00 0.00 4.35
482 518 4.036498 CGTCATCATAGAGTTAGGGTTCGT 59.964 45.833 0.00 0.00 0.00 3.85
577 613 4.228912 AGAAAGGACTTTTCATGTTGCG 57.771 40.909 12.08 0.00 46.20 4.85
591 627 2.505405 TGTTGCGCATAAGGGTGTTTA 58.495 42.857 12.75 0.00 0.00 2.01
594 630 4.700692 TGTTGCGCATAAGGGTGTTTATTA 59.299 37.500 12.75 0.00 0.00 0.98
598 634 6.868622 TGCGCATAAGGGTGTTTATTATTTT 58.131 32.000 5.66 0.00 0.00 1.82
599 635 7.324178 TGCGCATAAGGGTGTTTATTATTTTT 58.676 30.769 5.66 0.00 0.00 1.94
601 637 7.042992 GCGCATAAGGGTGTTTATTATTTTTCC 60.043 37.037 0.30 0.00 0.00 3.13
642 678 3.878699 TGGTTAAAACTGACGGAAAGGTC 59.121 43.478 0.00 0.00 37.45 3.85
748 785 7.020827 AGTCAAATAAGGAATTGTCTCCAGA 57.979 36.000 0.00 0.00 38.02 3.86
749 786 7.637511 AGTCAAATAAGGAATTGTCTCCAGAT 58.362 34.615 0.00 0.00 38.02 2.90
750 787 7.772757 AGTCAAATAAGGAATTGTCTCCAGATC 59.227 37.037 0.00 0.00 38.02 2.75
751 788 7.772757 GTCAAATAAGGAATTGTCTCCAGATCT 59.227 37.037 0.00 0.00 38.02 2.75
823 875 4.821589 GCCGCCTCGAACCTCCAG 62.822 72.222 0.00 0.00 0.00 3.86
870 939 2.167487 GACGAGCTTTCTGGAGGAGATT 59.833 50.000 0.00 0.00 0.00 2.40
1581 1715 0.726452 GCGTCGATGATCGCCTAGTC 60.726 60.000 10.45 0.00 45.54 2.59
1592 1726 2.307768 TCGCCTAGTCGGAATTCTCAT 58.692 47.619 5.23 0.00 33.16 2.90
1602 1736 5.516996 GTCGGAATTCTCATGTACGACATA 58.483 41.667 19.50 0.00 45.81 2.29
1942 2132 5.238214 CAGTGGAAGGAGAGAAAAGTTTCAG 59.762 44.000 6.56 0.00 39.61 3.02
1959 2149 5.476945 AGTTTCAGGTTTTCATCCCATACAC 59.523 40.000 0.00 0.00 0.00 2.90
2009 2731 9.832445 TGTTTGTATCTATATGTCCTTTCTTCC 57.168 33.333 0.00 0.00 0.00 3.46
2260 2995 0.654472 CGCGGCGCATTAAGAATGTC 60.654 55.000 32.61 0.00 41.01 3.06
2327 3074 1.072266 ACTTGGAGGCAACATGGGTA 58.928 50.000 0.00 0.00 41.41 3.69
2428 3176 4.315803 TGGTAGCTTTTGTCAGTTAGCTC 58.684 43.478 0.00 3.02 42.60 4.09
2961 3790 3.146066 GGAGCTAATGTGACAACCAACA 58.854 45.455 0.00 0.00 0.00 3.33
2962 3791 3.568007 GGAGCTAATGTGACAACCAACAA 59.432 43.478 0.00 0.00 0.00 2.83
2963 3792 4.218417 GGAGCTAATGTGACAACCAACAAT 59.782 41.667 0.00 0.00 0.00 2.71
2964 3793 5.278957 GGAGCTAATGTGACAACCAACAATT 60.279 40.000 0.00 0.00 0.00 2.32
2965 3794 5.531634 AGCTAATGTGACAACCAACAATTG 58.468 37.500 3.24 3.24 0.00 2.32
2966 3795 4.150451 GCTAATGTGACAACCAACAATTGC 59.850 41.667 5.05 0.00 0.00 3.56
2967 3796 3.815856 ATGTGACAACCAACAATTGCA 57.184 38.095 5.05 0.00 0.00 4.08
2968 3797 3.162202 TGTGACAACCAACAATTGCAG 57.838 42.857 5.05 0.00 0.00 4.41
2969 3798 2.495270 TGTGACAACCAACAATTGCAGT 59.505 40.909 5.05 0.00 0.00 4.40
2970 3799 3.696548 TGTGACAACCAACAATTGCAGTA 59.303 39.130 5.05 0.00 0.00 2.74
2971 3800 4.340666 TGTGACAACCAACAATTGCAGTAT 59.659 37.500 5.05 0.00 0.00 2.12
2972 3801 5.163468 TGTGACAACCAACAATTGCAGTATT 60.163 36.000 5.05 0.00 0.00 1.89
2973 3802 5.175491 GTGACAACCAACAATTGCAGTATTG 59.825 40.000 5.05 9.15 40.53 1.90
2975 3804 6.039829 TGACAACCAACAATTGCAGTATTGTA 59.960 34.615 15.35 0.00 45.44 2.41
2976 3805 6.446318 ACAACCAACAATTGCAGTATTGTAG 58.554 36.000 15.35 12.60 45.44 2.74
2977 3806 6.264292 ACAACCAACAATTGCAGTATTGTAGA 59.736 34.615 15.35 0.00 45.44 2.59
2978 3807 6.500684 ACCAACAATTGCAGTATTGTAGAG 57.499 37.500 15.35 10.37 45.44 2.43
2979 3808 5.415701 ACCAACAATTGCAGTATTGTAGAGG 59.584 40.000 15.35 17.49 45.44 3.69
2980 3809 5.335127 CAACAATTGCAGTATTGTAGAGGC 58.665 41.667 15.35 0.00 45.44 4.70
2981 3810 4.848357 ACAATTGCAGTATTGTAGAGGCT 58.152 39.130 13.80 0.00 44.62 4.58
2982 3811 5.256474 ACAATTGCAGTATTGTAGAGGCTT 58.744 37.500 13.80 0.00 44.62 4.35
2983 3812 5.711976 ACAATTGCAGTATTGTAGAGGCTTT 59.288 36.000 13.80 0.00 44.62 3.51
2984 3813 6.127897 ACAATTGCAGTATTGTAGAGGCTTTC 60.128 38.462 13.80 0.00 44.62 2.62
2985 3814 4.551702 TGCAGTATTGTAGAGGCTTTCA 57.448 40.909 0.00 0.00 0.00 2.69
2986 3815 4.507710 TGCAGTATTGTAGAGGCTTTCAG 58.492 43.478 0.00 0.00 0.00 3.02
2987 3816 4.222810 TGCAGTATTGTAGAGGCTTTCAGA 59.777 41.667 0.00 0.00 0.00 3.27
2988 3817 5.104776 TGCAGTATTGTAGAGGCTTTCAGAT 60.105 40.000 0.00 0.00 0.00 2.90
2989 3818 5.236047 GCAGTATTGTAGAGGCTTTCAGATG 59.764 44.000 0.00 0.00 0.00 2.90
2990 3819 6.344500 CAGTATTGTAGAGGCTTTCAGATGT 58.656 40.000 0.00 0.00 0.00 3.06
2991 3820 6.257411 CAGTATTGTAGAGGCTTTCAGATGTG 59.743 42.308 0.00 0.00 0.00 3.21
2992 3821 2.977914 TGTAGAGGCTTTCAGATGTGC 58.022 47.619 0.00 0.00 0.00 4.57
2993 3822 2.284190 GTAGAGGCTTTCAGATGTGCC 58.716 52.381 0.00 0.00 45.21 5.01
2996 3825 2.093216 GGCTTTCAGATGTGCCTCG 58.907 57.895 0.00 0.00 41.92 4.63
2997 3826 1.427020 GCTTTCAGATGTGCCTCGC 59.573 57.895 0.00 0.00 0.00 5.03
2998 3827 1.023513 GCTTTCAGATGTGCCTCGCT 61.024 55.000 0.00 0.00 0.00 4.93
2999 3828 1.005340 CTTTCAGATGTGCCTCGCTC 58.995 55.000 0.00 0.00 0.00 5.03
3000 3829 0.610174 TTTCAGATGTGCCTCGCTCT 59.390 50.000 0.00 0.00 0.00 4.09
3001 3830 1.474330 TTCAGATGTGCCTCGCTCTA 58.526 50.000 0.00 0.00 0.00 2.43
3002 3831 0.741326 TCAGATGTGCCTCGCTCTAC 59.259 55.000 0.00 0.00 0.00 2.59
3003 3832 0.249238 CAGATGTGCCTCGCTCTACC 60.249 60.000 0.00 0.00 0.00 3.18
3004 3833 0.396417 AGATGTGCCTCGCTCTACCT 60.396 55.000 0.00 0.00 0.00 3.08
3005 3834 0.249238 GATGTGCCTCGCTCTACCTG 60.249 60.000 0.00 0.00 0.00 4.00
3006 3835 0.972983 ATGTGCCTCGCTCTACCTGT 60.973 55.000 0.00 0.00 0.00 4.00
3007 3836 0.323087 TGTGCCTCGCTCTACCTGTA 60.323 55.000 0.00 0.00 0.00 2.74
3008 3837 1.033574 GTGCCTCGCTCTACCTGTAT 58.966 55.000 0.00 0.00 0.00 2.29
3009 3838 1.032794 TGCCTCGCTCTACCTGTATG 58.967 55.000 0.00 0.00 0.00 2.39
3010 3839 1.033574 GCCTCGCTCTACCTGTATGT 58.966 55.000 0.00 0.00 0.00 2.29
3011 3840 2.228059 GCCTCGCTCTACCTGTATGTA 58.772 52.381 0.00 0.00 0.00 2.29
3012 3841 2.621998 GCCTCGCTCTACCTGTATGTAA 59.378 50.000 0.00 0.00 0.00 2.41
3013 3842 3.550436 GCCTCGCTCTACCTGTATGTAAC 60.550 52.174 0.00 0.00 0.00 2.50
3014 3843 3.884091 CCTCGCTCTACCTGTATGTAACT 59.116 47.826 0.00 0.00 0.00 2.24
3015 3844 5.061853 CCTCGCTCTACCTGTATGTAACTA 58.938 45.833 0.00 0.00 0.00 2.24
3016 3845 5.179742 CCTCGCTCTACCTGTATGTAACTAG 59.820 48.000 0.00 0.00 0.00 2.57
3017 3846 4.514441 TCGCTCTACCTGTATGTAACTAGC 59.486 45.833 0.00 0.00 0.00 3.42
3018 3847 4.515944 CGCTCTACCTGTATGTAACTAGCT 59.484 45.833 0.00 0.00 0.00 3.32
3019 3848 5.334260 CGCTCTACCTGTATGTAACTAGCTC 60.334 48.000 0.00 0.00 0.00 4.09
3020 3849 5.766174 GCTCTACCTGTATGTAACTAGCTCT 59.234 44.000 0.00 0.00 0.00 4.09
3021 3850 6.072893 GCTCTACCTGTATGTAACTAGCTCTC 60.073 46.154 0.00 0.00 0.00 3.20
3022 3851 6.896883 TCTACCTGTATGTAACTAGCTCTCA 58.103 40.000 0.00 0.00 0.00 3.27
3023 3852 7.344134 TCTACCTGTATGTAACTAGCTCTCAA 58.656 38.462 0.00 0.00 0.00 3.02
3024 3853 6.458232 ACCTGTATGTAACTAGCTCTCAAG 57.542 41.667 0.00 0.00 0.00 3.02
3035 3864 2.985957 GCTCTCAAGCCTGAAGATCT 57.014 50.000 0.00 0.00 43.10 2.75
3036 3865 2.553086 GCTCTCAAGCCTGAAGATCTG 58.447 52.381 0.00 0.00 43.10 2.90
3037 3866 2.093553 GCTCTCAAGCCTGAAGATCTGT 60.094 50.000 0.00 0.00 43.10 3.41
3038 3867 3.131933 GCTCTCAAGCCTGAAGATCTGTA 59.868 47.826 0.00 0.00 43.10 2.74
3039 3868 4.382470 GCTCTCAAGCCTGAAGATCTGTAA 60.382 45.833 0.00 0.00 43.10 2.41
3040 3869 5.078411 TCTCAAGCCTGAAGATCTGTAAC 57.922 43.478 0.00 0.00 0.00 2.50
3041 3870 4.774726 TCTCAAGCCTGAAGATCTGTAACT 59.225 41.667 0.00 0.00 0.00 2.24
3042 3871 5.247110 TCTCAAGCCTGAAGATCTGTAACTT 59.753 40.000 0.00 0.00 0.00 2.66
3043 3872 6.437477 TCTCAAGCCTGAAGATCTGTAACTTA 59.563 38.462 0.00 0.00 0.00 2.24
3044 3873 6.398918 TCAAGCCTGAAGATCTGTAACTTAC 58.601 40.000 0.00 0.00 0.00 2.34
3045 3874 6.014584 TCAAGCCTGAAGATCTGTAACTTACA 60.015 38.462 0.00 1.67 37.13 2.41
3068 3897 7.593825 ACAGTGTTCTAATGAATAAAACAGCC 58.406 34.615 0.00 0.00 34.40 4.85
3069 3898 7.029563 CAGTGTTCTAATGAATAAAACAGCCC 58.970 38.462 0.00 0.00 34.40 5.19
3070 3899 6.152831 AGTGTTCTAATGAATAAAACAGCCCC 59.847 38.462 0.00 0.00 34.40 5.80
3071 3900 6.152831 GTGTTCTAATGAATAAAACAGCCCCT 59.847 38.462 0.00 0.00 34.40 4.79
3072 3901 6.723977 TGTTCTAATGAATAAAACAGCCCCTT 59.276 34.615 0.00 0.00 34.40 3.95
3073 3902 7.891183 TGTTCTAATGAATAAAACAGCCCCTTA 59.109 33.333 0.00 0.00 34.40 2.69
3074 3903 8.914011 GTTCTAATGAATAAAACAGCCCCTTAT 58.086 33.333 0.00 0.00 34.40 1.73
3075 3904 9.487442 TTCTAATGAATAAAACAGCCCCTTATT 57.513 29.630 0.00 0.00 0.00 1.40
3076 3905 9.131791 TCTAATGAATAAAACAGCCCCTTATTC 57.868 33.333 6.78 6.78 40.26 1.75
3077 3906 5.828299 TGAATAAAACAGCCCCTTATTCG 57.172 39.130 8.47 0.00 41.67 3.34
3078 3907 4.097286 TGAATAAAACAGCCCCTTATTCGC 59.903 41.667 8.47 0.00 41.67 4.70
3079 3908 1.917872 AAAACAGCCCCTTATTCGCA 58.082 45.000 0.00 0.00 0.00 5.10
3080 3909 1.917872 AAACAGCCCCTTATTCGCAA 58.082 45.000 0.00 0.00 0.00 4.85
3081 3910 1.917872 AACAGCCCCTTATTCGCAAA 58.082 45.000 0.00 0.00 0.00 3.68
3082 3911 1.917872 ACAGCCCCTTATTCGCAAAA 58.082 45.000 0.00 0.00 0.00 2.44
3083 3912 2.243810 ACAGCCCCTTATTCGCAAAAA 58.756 42.857 0.00 0.00 0.00 1.94
3135 3964 9.658799 TTTCATAAGAAAAACCACAAATCACAA 57.341 25.926 0.00 0.00 40.61 3.33
3136 3965 8.870160 TCATAAGAAAAACCACAAATCACAAG 57.130 30.769 0.00 0.00 0.00 3.16
3137 3966 8.690884 TCATAAGAAAAACCACAAATCACAAGA 58.309 29.630 0.00 0.00 0.00 3.02
3138 3967 8.971321 CATAAGAAAAACCACAAATCACAAGAG 58.029 33.333 0.00 0.00 0.00 2.85
3139 3968 6.773976 AGAAAAACCACAAATCACAAGAGA 57.226 33.333 0.00 0.00 0.00 3.10
3140 3969 6.799512 AGAAAAACCACAAATCACAAGAGAG 58.200 36.000 0.00 0.00 0.00 3.20
3141 3970 6.603201 AGAAAAACCACAAATCACAAGAGAGA 59.397 34.615 0.00 0.00 0.00 3.10
3142 3971 5.757850 AAACCACAAATCACAAGAGAGAC 57.242 39.130 0.00 0.00 0.00 3.36
3143 3972 3.393800 ACCACAAATCACAAGAGAGACG 58.606 45.455 0.00 0.00 0.00 4.18
3144 3973 2.738846 CCACAAATCACAAGAGAGACGG 59.261 50.000 0.00 0.00 0.00 4.79
3145 3974 3.393800 CACAAATCACAAGAGAGACGGT 58.606 45.455 0.00 0.00 0.00 4.83
3146 3975 3.430218 CACAAATCACAAGAGAGACGGTC 59.570 47.826 0.00 0.00 0.00 4.79
3147 3976 2.638556 AATCACAAGAGAGACGGTCG 57.361 50.000 1.89 0.00 0.00 4.79
3148 3977 1.822506 ATCACAAGAGAGACGGTCGA 58.177 50.000 1.89 0.00 0.00 4.20
3149 3978 1.157585 TCACAAGAGAGACGGTCGAG 58.842 55.000 1.89 0.00 0.00 4.04
3150 3979 1.157585 CACAAGAGAGACGGTCGAGA 58.842 55.000 1.89 0.00 0.00 4.04
3151 3980 1.740585 CACAAGAGAGACGGTCGAGAT 59.259 52.381 1.89 0.00 0.00 2.75
3152 3981 1.740585 ACAAGAGAGACGGTCGAGATG 59.259 52.381 1.89 2.94 0.00 2.90
3153 3982 2.010497 CAAGAGAGACGGTCGAGATGA 58.990 52.381 1.89 0.00 0.00 2.92
3160 3989 3.535691 CGGTCGAGATGACTGTAGC 57.464 57.895 0.00 0.00 46.93 3.58
3161 3990 0.733150 CGGTCGAGATGACTGTAGCA 59.267 55.000 0.00 0.00 46.93 3.49
3162 3991 1.268285 CGGTCGAGATGACTGTAGCAG 60.268 57.143 0.00 0.00 46.93 4.24
3163 3992 1.833860 GTCGAGATGACTGTAGCAGC 58.166 55.000 0.00 0.00 44.58 5.25
3164 3993 0.741326 TCGAGATGACTGTAGCAGCC 59.259 55.000 0.00 0.00 34.37 4.85
3165 3994 0.457443 CGAGATGACTGTAGCAGCCA 59.543 55.000 0.00 0.00 34.37 4.75
3166 3995 1.800655 CGAGATGACTGTAGCAGCCAC 60.801 57.143 0.00 0.00 34.37 5.01
3167 3996 0.174389 AGATGACTGTAGCAGCCACG 59.826 55.000 0.00 0.00 34.37 4.94
3168 3997 0.807667 GATGACTGTAGCAGCCACGG 60.808 60.000 0.00 0.00 34.37 4.94
3169 3998 2.815647 GACTGTAGCAGCCACGGC 60.816 66.667 0.00 0.00 42.33 5.68
3179 4008 3.499737 GCCACGGCGAATGGTCAG 61.500 66.667 16.62 0.00 39.63 3.51
3180 4009 2.264480 CCACGGCGAATGGTCAGA 59.736 61.111 16.62 0.00 32.08 3.27
3181 4010 1.811266 CCACGGCGAATGGTCAGAG 60.811 63.158 16.62 0.00 32.08 3.35
3182 4011 2.125512 ACGGCGAATGGTCAGAGC 60.126 61.111 16.62 0.00 0.00 4.09
3183 4012 2.185350 CGGCGAATGGTCAGAGCT 59.815 61.111 0.00 0.00 0.00 4.09
3184 4013 1.448540 CGGCGAATGGTCAGAGCTT 60.449 57.895 0.00 0.00 0.00 3.74
3185 4014 1.424493 CGGCGAATGGTCAGAGCTTC 61.424 60.000 0.00 2.10 0.00 3.86
3186 4015 0.391661 GGCGAATGGTCAGAGCTTCA 60.392 55.000 0.38 0.00 0.00 3.02
3187 4016 1.005340 GCGAATGGTCAGAGCTTCAG 58.995 55.000 0.38 1.79 0.00 3.02
3188 4017 1.674221 GCGAATGGTCAGAGCTTCAGT 60.674 52.381 0.38 0.00 0.00 3.41
3189 4018 1.998315 CGAATGGTCAGAGCTTCAGTG 59.002 52.381 0.38 0.00 0.00 3.66
3190 4019 2.354259 GAATGGTCAGAGCTTCAGTGG 58.646 52.381 0.38 0.00 0.00 4.00
3191 4020 0.617413 ATGGTCAGAGCTTCAGTGGG 59.383 55.000 0.38 0.00 0.00 4.61
3192 4021 0.471780 TGGTCAGAGCTTCAGTGGGA 60.472 55.000 0.38 0.00 0.00 4.37
3193 4022 0.908198 GGTCAGAGCTTCAGTGGGAT 59.092 55.000 0.00 0.00 0.00 3.85
3194 4023 1.280421 GGTCAGAGCTTCAGTGGGATT 59.720 52.381 0.00 0.00 0.00 3.01
3195 4024 2.290577 GGTCAGAGCTTCAGTGGGATTT 60.291 50.000 0.00 0.00 0.00 2.17
3196 4025 2.746362 GTCAGAGCTTCAGTGGGATTTG 59.254 50.000 0.00 0.00 0.00 2.32
3197 4026 2.373169 TCAGAGCTTCAGTGGGATTTGT 59.627 45.455 0.00 0.00 0.00 2.83
3198 4027 2.746362 CAGAGCTTCAGTGGGATTTGTC 59.254 50.000 0.00 0.00 0.00 3.18
3199 4028 1.734465 GAGCTTCAGTGGGATTTGTCG 59.266 52.381 0.00 0.00 0.00 4.35
3200 4029 1.072331 AGCTTCAGTGGGATTTGTCGT 59.928 47.619 0.00 0.00 0.00 4.34
3201 4030 1.464997 GCTTCAGTGGGATTTGTCGTC 59.535 52.381 0.00 0.00 0.00 4.20
3202 4031 2.766313 CTTCAGTGGGATTTGTCGTCA 58.234 47.619 0.00 0.00 0.00 4.35
3203 4032 2.455674 TCAGTGGGATTTGTCGTCAG 57.544 50.000 0.00 0.00 0.00 3.51
3204 4033 0.798776 CAGTGGGATTTGTCGTCAGC 59.201 55.000 0.00 0.00 0.00 4.26
3205 4034 0.687354 AGTGGGATTTGTCGTCAGCT 59.313 50.000 0.00 0.00 0.00 4.24
3206 4035 1.899814 AGTGGGATTTGTCGTCAGCTA 59.100 47.619 0.00 0.00 0.00 3.32
3207 4036 2.501723 AGTGGGATTTGTCGTCAGCTAT 59.498 45.455 0.00 0.00 0.00 2.97
3208 4037 3.704566 AGTGGGATTTGTCGTCAGCTATA 59.295 43.478 0.00 0.00 0.00 1.31
3209 4038 4.345257 AGTGGGATTTGTCGTCAGCTATAT 59.655 41.667 0.00 0.00 0.00 0.86
3210 4039 5.057149 GTGGGATTTGTCGTCAGCTATATT 58.943 41.667 0.00 0.00 0.00 1.28
3211 4040 6.041637 AGTGGGATTTGTCGTCAGCTATATTA 59.958 38.462 0.00 0.00 0.00 0.98
3212 4041 6.366332 GTGGGATTTGTCGTCAGCTATATTAG 59.634 42.308 0.00 0.00 0.00 1.73
3233 4062 8.798859 ATTAGCATGGATTGAATATACAGGAC 57.201 34.615 0.00 0.00 0.00 3.85
3234 4063 6.191657 AGCATGGATTGAATATACAGGACA 57.808 37.500 0.00 0.00 0.00 4.02
3235 4064 6.000219 AGCATGGATTGAATATACAGGACAC 59.000 40.000 0.00 0.00 0.00 3.67
3236 4065 6.000219 GCATGGATTGAATATACAGGACACT 59.000 40.000 0.00 0.00 0.00 3.55
3237 4066 6.148480 GCATGGATTGAATATACAGGACACTC 59.852 42.308 0.00 0.00 0.00 3.51
3238 4067 5.842907 TGGATTGAATATACAGGACACTCG 58.157 41.667 0.00 0.00 0.00 4.18
3239 4068 4.686554 GGATTGAATATACAGGACACTCGC 59.313 45.833 0.00 0.00 0.00 5.03
3240 4069 4.729227 TTGAATATACAGGACACTCGCA 57.271 40.909 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 9.950496 TCTTCTTCTCTAGCTTTCAAATACAAT 57.050 29.630 0.00 0.00 0.00 2.71
122 123 9.429359 CTCTTCTTCTCTAGCTTTCAAATACAA 57.571 33.333 0.00 0.00 0.00 2.41
123 124 8.037758 CCTCTTCTTCTCTAGCTTTCAAATACA 58.962 37.037 0.00 0.00 0.00 2.29
124 125 8.254508 TCCTCTTCTTCTCTAGCTTTCAAATAC 58.745 37.037 0.00 0.00 0.00 1.89
125 126 8.254508 GTCCTCTTCTTCTCTAGCTTTCAAATA 58.745 37.037 0.00 0.00 0.00 1.40
126 127 7.038373 AGTCCTCTTCTTCTCTAGCTTTCAAAT 60.038 37.037 0.00 0.00 0.00 2.32
127 128 6.268847 AGTCCTCTTCTTCTCTAGCTTTCAAA 59.731 38.462 0.00 0.00 0.00 2.69
128 129 5.777732 AGTCCTCTTCTTCTCTAGCTTTCAA 59.222 40.000 0.00 0.00 0.00 2.69
129 130 5.329399 AGTCCTCTTCTTCTCTAGCTTTCA 58.671 41.667 0.00 0.00 0.00 2.69
130 131 5.417580 TGAGTCCTCTTCTTCTCTAGCTTTC 59.582 44.000 0.00 0.00 0.00 2.62
131 132 5.185056 GTGAGTCCTCTTCTTCTCTAGCTTT 59.815 44.000 0.00 0.00 0.00 3.51
132 133 4.705023 GTGAGTCCTCTTCTTCTCTAGCTT 59.295 45.833 0.00 0.00 0.00 3.74
133 134 4.270008 GTGAGTCCTCTTCTTCTCTAGCT 58.730 47.826 0.00 0.00 0.00 3.32
134 135 3.380320 GGTGAGTCCTCTTCTTCTCTAGC 59.620 52.174 0.00 0.00 0.00 3.42
135 136 3.951680 GGGTGAGTCCTCTTCTTCTCTAG 59.048 52.174 0.00 0.00 36.25 2.43
136 137 3.594232 AGGGTGAGTCCTCTTCTTCTCTA 59.406 47.826 0.00 0.00 36.25 2.43
137 138 2.381961 AGGGTGAGTCCTCTTCTTCTCT 59.618 50.000 0.00 0.00 36.25 3.10
138 139 2.815158 AGGGTGAGTCCTCTTCTTCTC 58.185 52.381 0.00 0.00 36.25 2.87
139 140 3.169908 GAAGGGTGAGTCCTCTTCTTCT 58.830 50.000 11.80 0.00 38.87 2.85
140 141 2.094442 CGAAGGGTGAGTCCTCTTCTTC 60.094 54.545 15.19 11.17 39.32 2.87
141 142 1.896465 CGAAGGGTGAGTCCTCTTCTT 59.104 52.381 15.19 5.87 39.32 2.52
142 143 1.551452 CGAAGGGTGAGTCCTCTTCT 58.449 55.000 15.19 0.00 39.32 2.85
187 188 4.131088 GGTGGAGGAGGACGACGC 62.131 72.222 0.00 0.00 0.00 5.19
359 360 1.005748 CCAGAGAGCGTTCTGTGCA 60.006 57.895 19.19 0.00 41.96 4.57
367 368 1.594194 CTGCAGAGACCAGAGAGCGT 61.594 60.000 8.42 0.00 32.03 5.07
412 413 4.039092 AAGGCTGCTGCGGATGGT 62.039 61.111 13.72 0.00 40.82 3.55
443 444 2.345880 GACGACGATGGCGGTATGGT 62.346 60.000 0.00 0.00 43.17 3.55
450 451 1.069227 TCTATGATGACGACGATGGCG 60.069 52.381 0.00 0.00 44.79 5.69
454 455 4.456222 CCCTAACTCTATGATGACGACGAT 59.544 45.833 0.00 0.00 0.00 3.73
455 456 3.813724 CCCTAACTCTATGATGACGACGA 59.186 47.826 0.00 0.00 0.00 4.20
458 459 4.275196 CGAACCCTAACTCTATGATGACGA 59.725 45.833 0.00 0.00 0.00 4.20
463 499 4.099573 CCACACGAACCCTAACTCTATGAT 59.900 45.833 0.00 0.00 0.00 2.45
482 518 2.191400 CTTCTCTCCTGATTCCCCACA 58.809 52.381 0.00 0.00 0.00 4.17
548 584 1.061546 AAAGTCCTTTCTACCCCGCA 58.938 50.000 0.00 0.00 0.00 5.69
612 648 3.062369 CGTCAGTTTTAACCACGAACACA 59.938 43.478 8.32 0.00 37.71 3.72
660 696 5.586243 TCTTCCTCTTTTGACACTCAAACTG 59.414 40.000 0.00 0.00 45.03 3.16
710 747 8.630037 TCCTTATTTGACTTCTTTCTTGAAACC 58.370 33.333 0.00 0.00 0.00 3.27
715 752 9.971922 ACAATTCCTTATTTGACTTCTTTCTTG 57.028 29.630 0.00 0.00 0.00 3.02
740 777 3.333680 AGGGAGGAGATAGATCTGGAGAC 59.666 52.174 5.18 0.00 37.25 3.36
748 785 1.551329 GGCGGAAGGGAGGAGATAGAT 60.551 57.143 0.00 0.00 0.00 1.98
749 786 0.178958 GGCGGAAGGGAGGAGATAGA 60.179 60.000 0.00 0.00 0.00 1.98
750 787 1.528292 CGGCGGAAGGGAGGAGATAG 61.528 65.000 0.00 0.00 0.00 2.08
751 788 1.530891 CGGCGGAAGGGAGGAGATA 60.531 63.158 0.00 0.00 0.00 1.98
775 812 1.338105 GGTGGGGAATTTTTGAGCTGC 60.338 52.381 0.00 0.00 0.00 5.25
777 814 2.158325 TCTGGTGGGGAATTTTTGAGCT 60.158 45.455 0.00 0.00 0.00 4.09
778 815 2.247358 TCTGGTGGGGAATTTTTGAGC 58.753 47.619 0.00 0.00 0.00 4.26
781 818 3.495983 GGGTTTCTGGTGGGGAATTTTTG 60.496 47.826 0.00 0.00 0.00 2.44
870 939 2.056223 CGGCGGTAGGAGGAGGAAA 61.056 63.158 0.00 0.00 0.00 3.13
1257 1333 2.445845 ACCGCTGCCCCATAGCTA 60.446 61.111 0.00 0.00 39.00 3.32
1581 1715 5.107837 GCTTATGTCGTACATGAGAATTCCG 60.108 44.000 17.65 0.00 42.71 4.30
1942 2132 3.606687 ACTCGTGTATGGGATGAAAACC 58.393 45.455 0.00 0.00 0.00 3.27
1959 2149 5.924475 ACCTTGTGAATTGTAGAAACTCG 57.076 39.130 0.00 0.00 0.00 4.18
2008 2730 1.156736 GAGTTGTTCCCACATCACGG 58.843 55.000 0.00 0.00 31.06 4.94
2009 2731 2.169832 AGAGTTGTTCCCACATCACG 57.830 50.000 0.00 0.00 31.06 4.35
2260 2995 4.060038 AGCCTCGTACATATTCAACCAG 57.940 45.455 0.00 0.00 0.00 4.00
2327 3074 2.898729 ATTCATCAGGACTTCGCGAT 57.101 45.000 10.88 0.00 0.00 4.58
2428 3176 3.639538 CCACTAACACGGGAGATTATCG 58.360 50.000 0.00 0.00 0.00 2.92
2622 3372 4.508584 GGGAAACAGAAACCACTCCCTAAT 60.509 45.833 0.00 0.00 39.61 1.73
2737 3537 4.877823 TGCTATACTCTTCAGCAACATTGG 59.122 41.667 0.00 0.00 42.09 3.16
2859 3659 5.391097 CGAACACACACCAAACAGTTTTCTA 60.391 40.000 0.00 0.00 0.00 2.10
2961 3790 5.945784 TGAAAGCCTCTACAATACTGCAATT 59.054 36.000 0.00 0.00 0.00 2.32
2962 3791 5.500234 TGAAAGCCTCTACAATACTGCAAT 58.500 37.500 0.00 0.00 0.00 3.56
2963 3792 4.905429 TGAAAGCCTCTACAATACTGCAA 58.095 39.130 0.00 0.00 0.00 4.08
2964 3793 4.222810 TCTGAAAGCCTCTACAATACTGCA 59.777 41.667 0.00 0.00 0.00 4.41
2965 3794 4.759782 TCTGAAAGCCTCTACAATACTGC 58.240 43.478 0.00 0.00 0.00 4.40
2966 3795 6.257411 CACATCTGAAAGCCTCTACAATACTG 59.743 42.308 0.00 0.00 0.00 2.74
2967 3796 6.344500 CACATCTGAAAGCCTCTACAATACT 58.656 40.000 0.00 0.00 0.00 2.12
2968 3797 5.007136 GCACATCTGAAAGCCTCTACAATAC 59.993 44.000 0.00 0.00 0.00 1.89
2969 3798 5.118990 GCACATCTGAAAGCCTCTACAATA 58.881 41.667 0.00 0.00 0.00 1.90
2970 3799 3.944015 GCACATCTGAAAGCCTCTACAAT 59.056 43.478 0.00 0.00 0.00 2.71
2971 3800 3.338249 GCACATCTGAAAGCCTCTACAA 58.662 45.455 0.00 0.00 0.00 2.41
2972 3801 2.355108 GGCACATCTGAAAGCCTCTACA 60.355 50.000 10.08 0.00 43.70 2.74
2973 3802 2.284190 GGCACATCTGAAAGCCTCTAC 58.716 52.381 10.08 0.00 43.70 2.59
2974 3803 2.698855 GGCACATCTGAAAGCCTCTA 57.301 50.000 10.08 0.00 43.70 2.43
2975 3804 3.566130 GGCACATCTGAAAGCCTCT 57.434 52.632 10.08 0.00 43.70 3.69
2979 3808 1.023513 AGCGAGGCACATCTGAAAGC 61.024 55.000 0.00 0.00 0.00 3.51
2980 3809 1.005340 GAGCGAGGCACATCTGAAAG 58.995 55.000 0.00 0.00 0.00 2.62
2981 3810 0.610174 AGAGCGAGGCACATCTGAAA 59.390 50.000 0.00 0.00 0.00 2.69
2982 3811 1.135139 GTAGAGCGAGGCACATCTGAA 59.865 52.381 0.00 0.00 0.00 3.02
2983 3812 0.741326 GTAGAGCGAGGCACATCTGA 59.259 55.000 0.00 0.00 0.00 3.27
2984 3813 0.249238 GGTAGAGCGAGGCACATCTG 60.249 60.000 0.00 0.00 0.00 2.90
2985 3814 0.396417 AGGTAGAGCGAGGCACATCT 60.396 55.000 0.00 0.00 0.00 2.90
2986 3815 0.249238 CAGGTAGAGCGAGGCACATC 60.249 60.000 0.00 0.00 0.00 3.06
2987 3816 0.972983 ACAGGTAGAGCGAGGCACAT 60.973 55.000 0.00 0.00 0.00 3.21
2988 3817 0.323087 TACAGGTAGAGCGAGGCACA 60.323 55.000 0.00 0.00 0.00 4.57
2989 3818 1.033574 ATACAGGTAGAGCGAGGCAC 58.966 55.000 0.00 0.00 0.00 5.01
2990 3819 1.032794 CATACAGGTAGAGCGAGGCA 58.967 55.000 0.00 0.00 0.00 4.75
2991 3820 1.033574 ACATACAGGTAGAGCGAGGC 58.966 55.000 0.00 0.00 0.00 4.70
2992 3821 3.884091 AGTTACATACAGGTAGAGCGAGG 59.116 47.826 0.00 0.00 0.00 4.63
2993 3822 5.334260 GCTAGTTACATACAGGTAGAGCGAG 60.334 48.000 0.00 0.00 0.00 5.03
2994 3823 4.514441 GCTAGTTACATACAGGTAGAGCGA 59.486 45.833 0.00 0.00 0.00 4.93
2995 3824 4.515944 AGCTAGTTACATACAGGTAGAGCG 59.484 45.833 0.00 0.00 33.80 5.03
2996 3825 5.766174 AGAGCTAGTTACATACAGGTAGAGC 59.234 44.000 0.00 0.00 0.00 4.09
2997 3826 6.993308 TGAGAGCTAGTTACATACAGGTAGAG 59.007 42.308 0.00 0.00 0.00 2.43
2998 3827 6.896883 TGAGAGCTAGTTACATACAGGTAGA 58.103 40.000 0.00 0.00 0.00 2.59
2999 3828 7.569639 TTGAGAGCTAGTTACATACAGGTAG 57.430 40.000 0.00 0.00 0.00 3.18
3000 3829 6.039493 GCTTGAGAGCTAGTTACATACAGGTA 59.961 42.308 0.00 0.00 45.65 3.08
3001 3830 5.163499 GCTTGAGAGCTAGTTACATACAGGT 60.163 44.000 0.00 0.00 45.65 4.00
3002 3831 5.285651 GCTTGAGAGCTAGTTACATACAGG 58.714 45.833 0.00 0.00 45.65 4.00
3017 3846 3.891422 ACAGATCTTCAGGCTTGAGAG 57.109 47.619 0.00 0.51 34.15 3.20
3018 3847 4.774726 AGTTACAGATCTTCAGGCTTGAGA 59.225 41.667 0.00 0.00 34.15 3.27
3019 3848 5.083533 AGTTACAGATCTTCAGGCTTGAG 57.916 43.478 0.00 0.00 34.15 3.02
3020 3849 5.489792 AAGTTACAGATCTTCAGGCTTGA 57.510 39.130 0.00 0.00 0.00 3.02
3021 3850 6.166279 TGTAAGTTACAGATCTTCAGGCTTG 58.834 40.000 11.75 0.00 34.06 4.01
3022 3851 6.360370 TGTAAGTTACAGATCTTCAGGCTT 57.640 37.500 11.75 0.00 34.06 4.35
3042 3871 8.726988 GGCTGTTTTATTCATTAGAACACTGTA 58.273 33.333 0.00 0.00 36.39 2.74
3043 3872 7.309194 GGGCTGTTTTATTCATTAGAACACTGT 60.309 37.037 0.00 0.00 36.39 3.55
3044 3873 7.029563 GGGCTGTTTTATTCATTAGAACACTG 58.970 38.462 0.00 0.00 36.39 3.66
3045 3874 6.152831 GGGGCTGTTTTATTCATTAGAACACT 59.847 38.462 0.00 0.00 36.39 3.55
3046 3875 6.152831 AGGGGCTGTTTTATTCATTAGAACAC 59.847 38.462 0.00 0.00 36.39 3.32
3047 3876 6.252995 AGGGGCTGTTTTATTCATTAGAACA 58.747 36.000 0.00 0.00 36.39 3.18
3048 3877 6.775594 AGGGGCTGTTTTATTCATTAGAAC 57.224 37.500 0.00 0.00 36.39 3.01
3049 3878 9.487442 AATAAGGGGCTGTTTTATTCATTAGAA 57.513 29.630 0.00 0.00 38.31 2.10
3050 3879 9.131791 GAATAAGGGGCTGTTTTATTCATTAGA 57.868 33.333 9.93 0.00 40.74 2.10
3051 3880 8.076178 CGAATAAGGGGCTGTTTTATTCATTAG 58.924 37.037 13.45 0.00 40.93 1.73
3052 3881 7.469456 GCGAATAAGGGGCTGTTTTATTCATTA 60.469 37.037 13.45 0.00 40.93 1.90
3053 3882 6.682861 GCGAATAAGGGGCTGTTTTATTCATT 60.683 38.462 13.45 0.00 40.93 2.57
3054 3883 5.221244 GCGAATAAGGGGCTGTTTTATTCAT 60.221 40.000 13.45 0.00 40.93 2.57
3055 3884 4.097286 GCGAATAAGGGGCTGTTTTATTCA 59.903 41.667 13.45 0.00 40.93 2.57
3056 3885 4.097286 TGCGAATAAGGGGCTGTTTTATTC 59.903 41.667 0.00 6.26 39.04 1.75
3057 3886 4.020543 TGCGAATAAGGGGCTGTTTTATT 58.979 39.130 0.00 0.00 31.58 1.40
3058 3887 3.626930 TGCGAATAAGGGGCTGTTTTAT 58.373 40.909 0.00 0.00 0.00 1.40
3059 3888 3.074675 TGCGAATAAGGGGCTGTTTTA 57.925 42.857 0.00 0.00 0.00 1.52
3060 3889 1.917872 TGCGAATAAGGGGCTGTTTT 58.082 45.000 0.00 0.00 0.00 2.43
3061 3890 1.917872 TTGCGAATAAGGGGCTGTTT 58.082 45.000 0.00 0.00 0.00 2.83
3062 3891 1.917872 TTTGCGAATAAGGGGCTGTT 58.082 45.000 0.00 0.00 0.00 3.16
3063 3892 1.917872 TTTTGCGAATAAGGGGCTGT 58.082 45.000 0.00 0.00 0.00 4.40
3108 3937 9.658799 TGTGATTTGTGGTTTTTCTTATGAAAA 57.341 25.926 11.39 11.39 46.63 2.29
3109 3938 9.658799 TTGTGATTTGTGGTTTTTCTTATGAAA 57.341 25.926 0.00 0.00 40.08 2.69
3110 3939 9.311916 CTTGTGATTTGTGGTTTTTCTTATGAA 57.688 29.630 0.00 0.00 0.00 2.57
3111 3940 8.690884 TCTTGTGATTTGTGGTTTTTCTTATGA 58.309 29.630 0.00 0.00 0.00 2.15
3112 3941 8.870160 TCTTGTGATTTGTGGTTTTTCTTATG 57.130 30.769 0.00 0.00 0.00 1.90
3113 3942 8.912988 TCTCTTGTGATTTGTGGTTTTTCTTAT 58.087 29.630 0.00 0.00 0.00 1.73
3114 3943 8.287439 TCTCTTGTGATTTGTGGTTTTTCTTA 57.713 30.769 0.00 0.00 0.00 2.10
3115 3944 7.122650 TCTCTCTTGTGATTTGTGGTTTTTCTT 59.877 33.333 0.00 0.00 0.00 2.52
3116 3945 6.603201 TCTCTCTTGTGATTTGTGGTTTTTCT 59.397 34.615 0.00 0.00 0.00 2.52
3117 3946 6.693113 GTCTCTCTTGTGATTTGTGGTTTTTC 59.307 38.462 0.00 0.00 0.00 2.29
3118 3947 6.564328 GTCTCTCTTGTGATTTGTGGTTTTT 58.436 36.000 0.00 0.00 0.00 1.94
3119 3948 5.220854 CGTCTCTCTTGTGATTTGTGGTTTT 60.221 40.000 0.00 0.00 0.00 2.43
3120 3949 4.273480 CGTCTCTCTTGTGATTTGTGGTTT 59.727 41.667 0.00 0.00 0.00 3.27
3121 3950 3.809832 CGTCTCTCTTGTGATTTGTGGTT 59.190 43.478 0.00 0.00 0.00 3.67
3122 3951 3.393800 CGTCTCTCTTGTGATTTGTGGT 58.606 45.455 0.00 0.00 0.00 4.16
3123 3952 2.738846 CCGTCTCTCTTGTGATTTGTGG 59.261 50.000 0.00 0.00 0.00 4.17
3124 3953 3.393800 ACCGTCTCTCTTGTGATTTGTG 58.606 45.455 0.00 0.00 0.00 3.33
3125 3954 3.654414 GACCGTCTCTCTTGTGATTTGT 58.346 45.455 0.00 0.00 0.00 2.83
3126 3955 2.663602 CGACCGTCTCTCTTGTGATTTG 59.336 50.000 0.00 0.00 0.00 2.32
3127 3956 2.557056 TCGACCGTCTCTCTTGTGATTT 59.443 45.455 0.00 0.00 0.00 2.17
3128 3957 2.160205 TCGACCGTCTCTCTTGTGATT 58.840 47.619 0.00 0.00 0.00 2.57
3129 3958 1.740585 CTCGACCGTCTCTCTTGTGAT 59.259 52.381 0.00 0.00 0.00 3.06
3130 3959 1.157585 CTCGACCGTCTCTCTTGTGA 58.842 55.000 0.00 0.00 0.00 3.58
3131 3960 1.157585 TCTCGACCGTCTCTCTTGTG 58.842 55.000 0.00 0.00 0.00 3.33
3132 3961 1.740585 CATCTCGACCGTCTCTCTTGT 59.259 52.381 0.00 0.00 0.00 3.16
3133 3962 2.010497 TCATCTCGACCGTCTCTCTTG 58.990 52.381 0.00 0.00 0.00 3.02
3134 3963 2.011222 GTCATCTCGACCGTCTCTCTT 58.989 52.381 0.00 0.00 38.85 2.85
3135 3964 1.208535 AGTCATCTCGACCGTCTCTCT 59.791 52.381 0.00 0.00 46.69 3.10
3136 3965 1.329292 CAGTCATCTCGACCGTCTCTC 59.671 57.143 0.00 0.00 46.69 3.20
3137 3966 1.339247 ACAGTCATCTCGACCGTCTCT 60.339 52.381 0.00 0.00 46.69 3.10
3138 3967 1.088306 ACAGTCATCTCGACCGTCTC 58.912 55.000 0.00 0.00 46.69 3.36
3139 3968 2.281517 CTACAGTCATCTCGACCGTCT 58.718 52.381 0.00 0.00 46.69 4.18
3140 3969 1.268133 GCTACAGTCATCTCGACCGTC 60.268 57.143 0.00 0.00 46.69 4.79
3141 3970 0.733729 GCTACAGTCATCTCGACCGT 59.266 55.000 0.00 0.00 46.69 4.83
3142 3971 0.733150 TGCTACAGTCATCTCGACCG 59.267 55.000 0.00 0.00 46.69 4.79
3143 3972 1.535015 GCTGCTACAGTCATCTCGACC 60.535 57.143 0.00 0.00 46.69 4.79
3144 3973 1.535015 GGCTGCTACAGTCATCTCGAC 60.535 57.143 0.00 0.00 45.77 4.20
3145 3974 0.741326 GGCTGCTACAGTCATCTCGA 59.259 55.000 0.00 0.00 35.96 4.04
3146 3975 0.457443 TGGCTGCTACAGTCATCTCG 59.543 55.000 0.00 0.00 41.41 4.04
3151 3980 2.656646 CCGTGGCTGCTACAGTCA 59.343 61.111 16.46 0.00 44.22 3.41
3152 3981 2.815647 GCCGTGGCTGCTACAGTC 60.816 66.667 16.46 0.68 36.52 3.51
3153 3982 4.742201 CGCCGTGGCTGCTACAGT 62.742 66.667 16.46 0.00 39.32 3.55
3154 3983 3.932580 TTCGCCGTGGCTGCTACAG 62.933 63.158 16.46 5.97 39.32 2.74
3155 3984 3.309436 ATTCGCCGTGGCTGCTACA 62.309 57.895 16.46 0.00 39.32 2.74
3156 3985 2.511600 ATTCGCCGTGGCTGCTAC 60.512 61.111 9.55 6.02 39.32 3.58
3157 3986 2.511373 CATTCGCCGTGGCTGCTA 60.511 61.111 9.55 0.00 39.32 3.49
3160 3989 3.499737 GACCATTCGCCGTGGCTG 61.500 66.667 9.55 0.31 40.49 4.85
3161 3990 3.958147 CTGACCATTCGCCGTGGCT 62.958 63.158 9.55 0.00 40.49 4.75
3162 3991 3.499737 CTGACCATTCGCCGTGGC 61.500 66.667 0.00 0.00 40.49 5.01
3163 3992 1.811266 CTCTGACCATTCGCCGTGG 60.811 63.158 0.00 0.00 42.55 4.94
3164 3993 2.456119 GCTCTGACCATTCGCCGTG 61.456 63.158 0.00 0.00 0.00 4.94
3165 3994 2.125512 GCTCTGACCATTCGCCGT 60.126 61.111 0.00 0.00 0.00 5.68
3166 3995 1.424493 GAAGCTCTGACCATTCGCCG 61.424 60.000 0.00 0.00 0.00 6.46
3167 3996 0.391661 TGAAGCTCTGACCATTCGCC 60.392 55.000 0.00 0.00 0.00 5.54
3168 3997 1.005340 CTGAAGCTCTGACCATTCGC 58.995 55.000 0.00 0.00 0.00 4.70
3169 3998 1.998315 CACTGAAGCTCTGACCATTCG 59.002 52.381 0.00 0.00 0.00 3.34
3170 3999 2.354259 CCACTGAAGCTCTGACCATTC 58.646 52.381 0.00 0.00 0.00 2.67
3171 4000 1.004044 CCCACTGAAGCTCTGACCATT 59.996 52.381 0.00 0.00 0.00 3.16
3172 4001 0.617413 CCCACTGAAGCTCTGACCAT 59.383 55.000 0.00 0.00 0.00 3.55
3173 4002 0.471780 TCCCACTGAAGCTCTGACCA 60.472 55.000 0.00 0.00 0.00 4.02
3174 4003 0.908198 ATCCCACTGAAGCTCTGACC 59.092 55.000 0.00 0.00 0.00 4.02
3175 4004 2.746362 CAAATCCCACTGAAGCTCTGAC 59.254 50.000 0.00 0.00 0.00 3.51
3176 4005 2.373169 ACAAATCCCACTGAAGCTCTGA 59.627 45.455 0.00 0.00 0.00 3.27
3177 4006 2.746362 GACAAATCCCACTGAAGCTCTG 59.254 50.000 0.00 0.00 0.00 3.35
3178 4007 2.613977 CGACAAATCCCACTGAAGCTCT 60.614 50.000 0.00 0.00 0.00 4.09
3179 4008 1.734465 CGACAAATCCCACTGAAGCTC 59.266 52.381 0.00 0.00 0.00 4.09
3180 4009 1.072331 ACGACAAATCCCACTGAAGCT 59.928 47.619 0.00 0.00 0.00 3.74
3181 4010 1.464997 GACGACAAATCCCACTGAAGC 59.535 52.381 0.00 0.00 0.00 3.86
3182 4011 2.738846 CTGACGACAAATCCCACTGAAG 59.261 50.000 0.00 0.00 0.00 3.02
3183 4012 2.766313 CTGACGACAAATCCCACTGAA 58.234 47.619 0.00 0.00 0.00 3.02
3184 4013 1.608025 GCTGACGACAAATCCCACTGA 60.608 52.381 0.00 0.00 0.00 3.41
3185 4014 0.798776 GCTGACGACAAATCCCACTG 59.201 55.000 0.00 0.00 0.00 3.66
3186 4015 0.687354 AGCTGACGACAAATCCCACT 59.313 50.000 0.00 0.00 0.00 4.00
3187 4016 2.380084 TAGCTGACGACAAATCCCAC 57.620 50.000 0.00 0.00 0.00 4.61
3188 4017 4.955811 ATATAGCTGACGACAAATCCCA 57.044 40.909 0.00 0.00 0.00 4.37
3189 4018 6.952935 CTAATATAGCTGACGACAAATCCC 57.047 41.667 0.00 0.00 0.00 3.85
3207 4036 9.890629 GTCCTGTATATTCAATCCATGCTAATA 57.109 33.333 0.00 0.00 0.00 0.98
3208 4037 8.385491 TGTCCTGTATATTCAATCCATGCTAAT 58.615 33.333 0.00 0.00 0.00 1.73
3209 4038 7.661437 GTGTCCTGTATATTCAATCCATGCTAA 59.339 37.037 0.00 0.00 0.00 3.09
3210 4039 7.016563 AGTGTCCTGTATATTCAATCCATGCTA 59.983 37.037 0.00 0.00 0.00 3.49
3211 4040 6.000219 GTGTCCTGTATATTCAATCCATGCT 59.000 40.000 0.00 0.00 0.00 3.79
3212 4041 6.000219 AGTGTCCTGTATATTCAATCCATGC 59.000 40.000 0.00 0.00 0.00 4.06
3213 4042 6.367149 CGAGTGTCCTGTATATTCAATCCATG 59.633 42.308 0.00 0.00 0.00 3.66
3214 4043 6.459066 CGAGTGTCCTGTATATTCAATCCAT 58.541 40.000 0.00 0.00 0.00 3.41
3215 4044 5.739070 GCGAGTGTCCTGTATATTCAATCCA 60.739 44.000 0.00 0.00 0.00 3.41
3216 4045 4.686554 GCGAGTGTCCTGTATATTCAATCC 59.313 45.833 0.00 0.00 0.00 3.01
3217 4046 5.289595 TGCGAGTGTCCTGTATATTCAATC 58.710 41.667 0.00 0.00 0.00 2.67
3218 4047 5.276461 TGCGAGTGTCCTGTATATTCAAT 57.724 39.130 0.00 0.00 0.00 2.57
3219 4048 4.729227 TGCGAGTGTCCTGTATATTCAA 57.271 40.909 0.00 0.00 0.00 2.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.